This page was generated on 2023-05-26 06:18:04 -0000 (Fri, 26 May 2023).
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### Running command:
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### /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data BBCAnalyzer
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* checking for file ‘BBCAnalyzer/DESCRIPTION’ ... OK
* preparing ‘BBCAnalyzer’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... ERROR
--- re-building ‘BBCAnalyzer.Rnw’ using Sweave
Loading required package: BSgenome
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame,
basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep,
grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: rtracklayer
Determine Target
Analyze Reads
Sample 1 out of 2
Position 1 out of 7
Position 2 out of 7
Position 3 out of 7
Position 4 out of 7
Position 5 out of 7
Position 6 out of 7
Position 7 out of 7
Sample 2 out of 2
Position 1 out of 7
Position 2 out of 7
Position 3 out of 7
Position 4 out of 7
Position 5 out of 7
Position 6 out of 7
Position 7 out of 7
Analyze Frequency
Sample 1
Sample 2
Report Variants
Sample 1
Sample 2
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Warning in plot.window(xlim, ylim, log = log, ...) :
`mgp[1:3]' are of differing sign
Warning in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty = axis.lty, :
`mgp[1:3]' are of differing sign
Warning in title(main = main, sub = sub, xlab = xlab, ylab = ylab, ...) :
`mgp[1:3]' are of differing sign
Warning in axis(if (horiz) 1 else 2, cex.axis = cex.axis, ...) :
`mgp[1:3]' are of differing sign
Warning in plot.window(xlim, ylim, log = log, ...) :
`mgp[1:3]' are of differing sign
Warning in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty = axis.lty, :
`mgp[1:3]' are of differing sign
Warning in title(main = main, sub = sub, xlab = xlab, ylab = ylab, ...) :
`mgp[1:3]' are of differing sign
Warning in axis(if (horiz) 1 else 2, cex.axis = cex.axis, ...) :
`mgp[1:3]' are of differing sign
Error: processing vignette 'BBCAnalyzer.Rnw' failed with diagnostics:
unable to run pdflatex on 'BBCAnalyzer.tex'
LaTeX errors:
! LaTeX Error: File `textpos.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.9 \usepackage
{amssymb}^^M
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘BBCAnalyzer.Rnw’
SUMMARY: processing the following file failed:
‘BBCAnalyzer.Rnw’
Error: Vignette re-building failed.
Execution halted